9Q3F

Structure of neurodevelopmental mutant AGO1 F180del in complex with guide RNA

Summary for 9Q3F

• Entry DOI: 10.2210/pdb9q3f/pdb
• Related: 9Q3G
• EMDB information: 72192
• Descriptor: Protein argonaute-1, Non-homogenous guide RNA (2 entities in total)
• Functional Keywords: complex, mutant, gene regulation
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 101322.42

Authors

Savidge, A.,Adhav, V.,Shen, Z.,Fu, T.,Nakanishi, K. (deposition date: 2025-08-18, release date: 2025-11-05, Last modification date: 2026-05-06)

Primary citation

Savidge, A.,Zhang, H.,Annasaheb Adhav, V.,Kehling, A.C.,Sim, G.,Shen, Z.,Fu, T.M.,Nakanishi, K.
Neurodevelopmental disorder-linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3'→5' trimming.
Proc.Natl.Acad.Sci.USA, 122:e2524644122-e2524644122, 2025

PubMed Abstract: Mutations in Argonaute proteins (AGOs) cause Argonaute syndrome, a neurodevelopmental disorder (NDD), yet the underlying molecular mechanism remains unclear. We determined cryo-electron microscopy (cryo-EM) structures of wild-type (WT) AGO1 and the recurrent, severe causative ΔF180 mutant. AGO1(ΔF180) unexpectedly rearranges the hydrophobic core of the L1 domain to preserve the overall RNA-induced silencing complexes (RISC) architecture and recognize guide RNAs similarly to WT. Functionally, the mutant binds target RNAs like WT but more frequently retains passenger strands, implicating a defect in RISC assembly. Biochemical assays of ΔF180 and L190P mutants revealed normal duplex loading but impaired passenger ejection, exposing guide 3' ends to 3'→5' exonucleases and generating abnormally short ~11-nucleotide RNAs. In cells, AGO1(ΔF180), AGO1(G199S), and corresponding AGO2 mutants likewise produced truncated guides. Together, these findings support a model in which defective passenger ejection underlies the pathology of AGO-associated NDDs by rendering microRNAs bound to AGO syndrome mutants susceptible to aberrant 3' trimming.

PubMed: 41237208
DOI: 10.1073/pnas.2524644122

Experimental method

ELECTRON MICROSCOPY (3.3 Å)